In order to meet the long-term observation requirements of the Earth-Moon imaging spectrometers mounted on the high-altitude balloon platform, the thermal design was presented. The corresponding thermal environment of the load system was analyzed, the heat transfer model of the load system was established, and the sensitivity analysis of the main parameters affecting the temperature level of the load system was carried out by using Spearman rank correlation coefficient formula and the BP-Garson method combining backpropagation neural network with Garson formula. The thermal control pattern of the load system was depicted clearly. In addition, the finite element model of the load system was built and the spectrometers′ two working conditions, the December solstice and the June solstice conditions, was simulated by using the I-DEAS/TMG software. The simulation results indicate that under two working conditions, the spectrometers can quickly cool down to -5 ℃ within 2 h, and the spectrometers maintain the temperature level of (-5±2) ℃ for more than 3.5 h, the optical window temperature is higher than the local dew point temperature at the altitude of 20 km, which satisfies the requirements and the thermal design is reasonable. The research jobs could give some guidance and reference for other ball-loaded optical remote sensors.